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- EMDB-48600: Helical tail assembly of phage JohannRWettstein (Bas63) -

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Basic information

Entry
Database: EMDB / ID: EMD-48600
TitleHelical tail assembly of phage JohannRWettstein (Bas63)
Map data
Sample
  • Virus: JohannRWettstein (virus)
    • Protein or peptide: Tube protein
    • Protein or peptide: Structural protein
KeywordsTail / sheath / tube / phage / Bas63 / JohannRWettstein / VIRAL PROTEIN
Function / homologyStructural protein ORF10, bacteriophage KPP10 / Protein of unknown function DUF3383 / Bacteriophage PhiTE tail tube protein / Protein of unknown function (DUF3383) / Uncharacterized protein / Structural protein
Function and homology information
Biological speciesEscherichia phage JohannRWettstein (virus) / JohannRWettstein (virus)
Methodhelical reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsHodgkinson-Bean J
Funding support Japan, 2 items
OrganizationGrant numberCountry
Ministry of Agriculture, Forestry and Fisheries (MAFF)GD0696J004 Japan
Japan Society for the Promotion of Science (JSPS)21K20645 Japan
CitationJournal: Sci Adv / Year: 2025
Title: C12 local connector reconstruction of phage JohannRWettstein (Bas63)
Authors: Hodgkinson-Bean J / Ayala R / McJarrow-Keller K / Cassin L / Rutter GL / Crowe AJM / Wolf M / Bostina M
History
DepositionJan 10, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48600.png

Downloads & links

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Map

FileDownload / File: emd_48600.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 400 pix.
= 554.8 Å		1.39 Å/pix.
x 400 pix.
= 554.8 Å		1.39 Å/pix.
x 400 pix.
= 554.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.387 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.97
Minimum - Maximum-3.4714942 - 6.277869
Average (Standard dev.)0.01752766 (±0.23009315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 554.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48600_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48600_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : JohannRWettstein

EntireName: JohannRWettstein (virus)
Components
  • Virus: JohannRWettstein (virus)
    • Protein or peptide: Tube protein
    • Protein or peptide: Structural protein

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Supramolecule #1: JohannRWettstein

SupramoleculeName: JohannRWettstein / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2852035 / Sci species name: JohannRWettstein / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichi coli

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Macromolecule #1: Tube protein

MacromoleculeName: Tube protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 16.203184 KDa
SequenceString:
MAMYQQYSPK DVVCSWNGIA IEGFAPDSFL RLQRTSPLVT PVVGAGGQVA LTRNADKTGT IEIELMQTSL SNQMLSAIQA KQDNMELEE DISSNFVIYD PSGSVLATGI NAWLQELPQI ELGRDQNSKT WIFGCEKLDY TSTIPASSV

UniProtKB: Uncharacterized protein

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Macromolecule #2: Structural protein

MacromoleculeName: Structural protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 48.916574 KDa
SequenceString: MWNPIVNVDI TLNTAGTTRE GFGLPLFLAS TDNFEERVRG YTSLTEVAED FDENTAAYKA AKQLWSQTPK VTQLYIGRRA MQYTVSIPN AVTESTDYSI TVAAGGGISQ PYQYTAQAED TAENVLQQFK TQIEADPTIK DKVSVNVTGS NGSATMIITK A GDNDFVKV ...String:
MWNPIVNVDI TLNTAGTTRE GFGLPLFLAS TDNFEERVRG YTSLTEVAED FDENTAAYKA AKQLWSQTPK VTQLYIGRRA MQYTVSIPN AVTESTDYSI TVAAGGGISQ PYQYTAQAED TAENVLQQFK TQIEADPTIK DKVSVNVTGS NGSATMIITK A GDNDFVKV TTTAQTVYIA STTADTASTA LAAIEAYSTD WYFIAAEDRT QQFVLAMASE IQARKKIFFT ANSDVTALQG TE LASANDV PAQLAKNMYT RTVCLWHHAA AEDYPEMAYI AYGAPYDAGS IAWGNAQLTG VAASLQPSNQ RPLTSIQKSA LDV RHCNFI DLDGGVPVVR RGITSGGEWI DIVRGVDWLE SDLKTSLRDL LINQKGGKIT YDDTGITRIR QVIETSLQRA VNRN FLSSY TVNVPKASQV ALADKKARIL KDVTFAGILA GAILDVDLKG TVAYE

UniProtKB: Structural protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 49.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 38.1 Å
Applied symmetry - Helical parameters - Δ&Phi: 25.9 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104888
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE

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